bio 1.0.0 → 1.1.0

data/lib/bio/db/transfac.rb

@@ -1,23 +1,11 @@
 #
-# bio/db/transfac.rb - TRANSFAC database class
+# = bio/db/transfac.rb - TRANSFAC database class
 #
-#   Copyright (C) 2001 KAWASHIMA Shuichi <s@bioruby.org>
+# Copyright::	Copyright (C) 2001
+#		Shuichi Kawashima <shuichi@hgc.jp>
+# License::	The Ruby License
 #
-#  This library is free software; you can redistribute it and/or
-#  modify it under the terms of the GNU Lesser General Public
-#  License as published by the Free Software Foundation; either
-#  version 2 of the License, or (at your option) any later version.
-#
-#  This library is distributed in the hope that it will be useful,
-#  but WITHOUT ANY WARRANTY; without even the implied warranty of
-#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-#  Lesser General Public License for more details.
-#
-#  You should have received a copy of the GNU Lesser General Public
-#  License along with this library; if not, write to the Free Software
-#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
-#
-#  $Id: transfac.rb,v 1.10 2005/11/28 04:57:33 k Exp $
+# $Id: transfac.rb,v 1.12 2007/04/05 23:35:40 trevor Exp $
 #
 
 require "bio/db"

data/lib/bio/feature.rb

@@ -1,51 +1,54 @@
 #
 # = bio/feature.rb - Features/Feature class (GenBank Feature table)
 #
-# Copyright::	Copyright (c) 2002, 2005
-#		Toshiaki Katayama <k@bioruby.org>
-# License::	Ruby's
-#
-# $Id: feature.rb,v 1.10 2006/02/27 09:13:46 k Exp $
-#
-# == INSD Feature table definition
-#
-# See http://www.ddbj.nig.ac.jp/FT/full_index.html for the INSD
-# (GenBank/EMBL/DDBJ) Feature table definition.
-#
-# === Example
-#
-#  # suppose features is a Bio::Features object
-#  features.each do |feature|
-#    f_name = feature.feature
-#    f_pos  = feature.position
-#    puts "#{f_name}:\t#{f_pos}"
-#    feature.each do |qualifier|
-#      q_name = qualifier.qualifier
-#      q_val  = qualifier.value
-#      puts "- #{q_name}:\t#{q_val}"
-#    end
-#  end
-#
-#  # Iterates only on CDS features and extract translated amino acid sequences
-#  features.each("CDS") do |feature|
-#    hash = feature.assoc
-#    name = hash["gene"] || hash["product"] || hash["note"] 
-#    seq  = hash["translation"]
-#    pos  = feature.position
-#    if gene and seq
-#      puts ">#{gene} #{feature.position}"
-#      puts aaseq
-#    end
-#  end
+# Copyright::	Copyright (c) 2002, 2005  Toshiaki Katayama <k@bioruby.org>
+#                             2006        Jan Aerts <jan.aerts@bbsrc.ac.uk>
+# License::	The Ruby License
 #
+# $Id: feature.rb,v 1.13 2007/04/05 23:35:39 trevor Exp $
 
 require 'bio/location'
 
 module Bio
 
+# = DESCRIPTION
 # Container for the sequence annotation.
+#
+# = USAGE
+#  # Create a Bio::Feature object.
+#  # For example: the GenBank-formatted entry in genbank for accession M33388
+#  # contains the following feature:
+#  #    exon     1532..1799
+#  #             /gene="CYP2D6"
+#  #             /note="cytochrome P450 IID6; GOO-132-127"
+#  #             /number="1"
+#  feature = Bio::Feature.new('exon','1532..1799')
+#  feature.append(Bio::Feature::Qualifier.new('gene', 'CYP2D6'))
+#  feature.append(Bio::Feature::Qualifier.new('note', 'cytochrome P450 IID6'))
+#  feature.append(Bio::Feature::Qualifier.new('number', '1'))
+#
+#  # or all in one go:
+#  feature2 = Bio::Feature.new('exon','1532..1799',
+#    [ Bio::Feature::Qualifier.new('gene', 'CYP2D6'),
+#      Bio::Feature::Qualifier.new('note', 'cytochrome P450 IID6; GOO-132-127'),
+#      Bio::Feature::Qualifier.new('number', '1')
+#    ])
+#
+#  # Print the feature
+#  puts feature.feature + "\t" + feature.position
+#  feature.each do |qualifier|
+#    puts "- " + qualifier.qualifier + ": " + qualifier.value
+#  end
+#
+# = REFERENCES
+# INSD feature table definition:: http://www.ddbj.nig.ac.jp/FT/full_index.html
 class Feature
-
+  # Create a new Bio::Feature object.
+  # *Arguments*:
+  # * (required) _feature_: type of feature (e.g. "exon")
+  # * (required) _position_: position of feature (e.g. "complement(1532..1799)")
+  # * (opt) _qualifiers_: list of Bio::Feature::Qualifier objects (default: [])
+  # *Returns*:: Bio::Feature object
   def initialize(feature = '', position = '', qualifiers = [])
     @feature, @position, @qualifiers = feature, position, qualifiers
   end
@@ -65,16 +68,19 @@ class Feature
   end
 
   # Appends a Qualifier object to the Feature.
-  #
-  # * Returns an Array of Qualifier objects.
-  # * If the argument is not a Qualifier object, returns nil.
-  #
+  # 
+  # *Arguments*:
+  # * (required) _qualifier_: Bio::Feature::Qualifier object
+  # *Returns*:: Bio::Feature object
   def append(a)
     @qualifiers.push(a) if a.is_a? Qualifier
     return self
   end
 
-  # Iterates on each qualifier.
+  # Iterates on each qualifier object.
+  #
+  # *Arguments*:
+  # * (optional) _key_: if specified, only iterates over qualifiers with this key
   def each(arg = nil)
     @qualifiers.each do |x|
       next if arg and x.qualifier != arg
@@ -107,9 +113,14 @@ class Feature
     self.to_hash[key]
   end
 
-  # Container for the qualifier-value pair.
+  # Container for qualifier-value pairs for sequence features.
   class Qualifier
-
+    # Creates a new Bio::Feature::Qualifier object
+    #
+    # *Arguments*:
+    # * (required) _key_: key of the qualifier (e.g. "gene")
+    # * (required) _value_: value of the qualifier (e.g. "CYP2D6")
+    # *Returns*:: Bio::Feature::Qualifier object
     def initialize(key, value)
       @qualifier, @value = key, value
     end
@@ -120,14 +131,52 @@ class Feature
     # Qualifier value in String
     attr_reader :value
 
-  end
+  end #Qualifier
 
-end
+end #Feature
 
 
-# Container for the list of Feature objects.
+# = DESCRIPTION
+# Container for a list of Feature objects.
+#
+# = USAGE
+#  # First, create some Bio::Feature objects
+#  feature1 = Bio::Feature.new('intron','3627..4059')
+#  feature2 = Bio::Feature.new('exon','4060..4236')
+#  feature3 = Bio::Feature.new('intron','4237..4426')
+#  feature4 = Bio::Feature.new('CDS','join(2538..3626,4060..4236)',
+#                   [ Bio::Feature::Qualifier.new('gene', 'CYP2D6'),
+#                     Bio::Feature::Qualifier.new('translation','MGXXTVMHLL...')
+#                   ])
+#
+#  # And create a container for them
+#  feature_container = Bio::Features.new([ feature1, feature2, feature3, feature4 ])
+#
+#  # Iterate over all features and print
+#  feature_container.each do |feature|
+#    puts feature.feature + "\t" + feature.position
+#    feature.each do |qualifier|
+#      puts "- " + qualifier.qualifier + ": " + qualifier.value
+#    end
+#  end
+#
+#  # Iterate only over CDS features and extract translated amino acid sequences
+#  features.each("CDS") do |feature|
+#    hash = feature.to_hash
+#    name = hash["gene"] || hash["product"] || hash["note"] 
+#    aaseq  = hash["translation"]
+#    pos  = feature.position
+#    if name and seq
+#      puts ">#{gene} #{feature.position}"
+#      puts aaseq
+#    end
+#  end
 class Features
-
+  # Create a new Bio::Features object.
+  #
+  # *Arguments*:
+  # * (optional) _list of features_: list of Bio::Feature objects
+  # *Returns*:: Bio::Features object
   def initialize(ary = [])
     @features = ary
   end
@@ -136,13 +185,19 @@ class Features
   attr_accessor :features
 
   # Appends a Feature object to Features.
+  # 
+  # *Arguments*:
+  # * (required) _feature_: Bio::Feature object
+  # *Returns*:: Bio::Features object
   def append(a)
     @features.push(a) if a.is_a? Feature
     return self
   end
 
-  # Iterates on each feature.  If a feature name is given as an argument,
-  # only iterates on each feature belongs to the name (e.g. 'CDS' etc.)
+  # Iterates on each feature object.
+  #
+  # *Arguments*:
+  # * (optional) _key_: if specified, only iterates over features with this key
   def each(arg = nil)
     @features.each do |x|
       next if arg and x.feature != arg
@@ -165,8 +220,7 @@ class Features
     @features.last
   end
 
-end
+end # Features
 
 end # Bio
 
-

data/lib/bio/io/das.rb

@@ -1,12 +1,12 @@
 #
 # = bio/io/das.rb - BioDAS access module
 #
-# Copyright::	Copyright (C) 2003, 2004
+# Copyright::	Copyright (C) 2003, 2004, 2007
 #		Shuichi Kawashima <shuichi@hgc.jp>,
 #		Toshiaki Katayama <k@bioruby.org>
-# License::	LGPL
+# License::	The Ruby License
 #
-# $Id: das.rb,v 1.11 2005/11/14 02:01:54 k Exp $
+# $Id: das.rb,v 1.17 2007/07/16 18:06:12 k Exp $
 #
 #--
 # == TODO
@@ -15,31 +15,12 @@
 #
 #++
 #
-#--
-#
-#  This library is free software; you can redistribute it and/or
-#  modify it under the terms of the GNU Lesser General Public
-#  License as published by the Free Software Foundation; either
-#  version 2 of the License, or (at your option) any later version.
-#
-#  This library is distributed in the hope that it will be useful,
-#  but WITHOUT ANY WARRANTY; without even the implied warranty of
-#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-#  Lesser General Public License for more details.
-#
-#  You should have received a copy of the GNU Lesser General Public
-#  License along with this library; if not, write to the Free Software
-#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
-#
-#++
-#
 
 begin
   require 'rexml/document'
 rescue LoadError
 end
-require 'uri'
-require 'net/http'
+require 'bio/command'
 require 'bio/sequence'
 
 
@@ -49,15 +30,24 @@ class DAS
 
   # Specify DAS server to connect
   def initialize(url = 'http://www.wormbase.org:80/db/')
-    schema, user, host, port, reg, path, = URI.split(url)
-    @server = Net::HTTP.new(host, port)
-    @prefix = path ? path.chomp('/') : ''
+    @server = url.chomp('/')
   end
 
+  def dna(dsn, entry_point, start, stop)
+    seg = Bio::DAS::SEGMENT.region(entry_point, start, stop)
+    self.get_dna(dsn, seg).first.sequence
+  end
+
+  def features(dsn, entry_point, start, stop)
+    seg = Bio::DAS::SEGMENT.region(entry_point, start, stop)
+    self.get_features(dsn, seg)
+  end
+
+
   # Returns an Array of Bio::DAS::DSN
   def get_dsn
     ary = []
-    result, = @server.get(@prefix + '/das/dsn')
+    result, = Bio::Command.post_form("#{@server}/das/dsn")
     doc = REXML::Document.new(result.body)
     doc.elements.each('/descendant::DSN') do |e|
       dsn = DSN.new
@@ -68,7 +58,7 @@ class DAS
           dsn.source_id = e.attributes['id']
           dsn.source_version = e.attributes['version']
         when 'MAPMASTER'
-          dsn.mapmaster = e.name
+          dsn.mapmaster = e.text
         when 'DESCRIPTION'
           dsn.description = e.text
           dsn.description_href = e.attributes['href']
@@ -81,10 +71,14 @@ class DAS
 
   # Returns Bio::DAS::ENTRY_POINT.
   # The 'dsn' can be a String or a Bio::DAS::DSN object.
-  def get_entry_point(dsn)
+  def get_entry_points(dsn)
     entry_point = ENTRY_POINT.new
-    dsn = dsn.source if dsn.instance_of?(Bio::DAS::DSN)
-    result, = @server.get(@prefix + '/das/' + dsn + '/entry_points')
+    if dsn.instance_of?(Bio::DAS::DSN)
+      src = dsn.source 
+    else
+      src = dsn
+    end
+    result, = Bio::Command.post_form("#{@server}/das/#{src}/entry_points")
     doc = REXML::Document.new(result.body)
     doc.elements.each('/descendant::ENTRY_POINTS') do |e|
       entry_point.href = e.attributes['href']
@@ -93,8 +87,8 @@ class DAS
         segment = SEGMENT.new
         segment.entry_id = e.attributes['id']
         segment.start = e.attributes['start']
-        segment.stop = e.attributes['stop']
-        segment.stop = e.attributes['orientation']
+        segment.stop = e.attributes['stop'] || e.attributes['size']
+        segment.orientation = e.attributes['orientation']
         segment.subparts = e.attributes['subparts']
         segment.description = e.text
         entry_point.segments << segment
@@ -117,9 +111,8 @@ class DAS
     segments.each do |s|
       opts << "segment=#{s.entry_id}:#{s.start},#{s.stop}"
     end
-    query = opts.join(';')
 
-    result, = @server.get(@prefix + '/das/' + dsn + '/dna?' + query)
+    result, = Bio::Command.post_form("#{@server}/das/#{dsn}/dna", opts)
     doc = REXML::Document.new(result.body)
     doc.elements.each('/descendant::SEQUENCE') do |e|
       sequence = DNA.new
@@ -150,9 +143,8 @@ class DAS
     segments.each do |s|
       opts << "segment=#{s.entry_id}:#{s.start},#{s.stop}"
     end
-    query = opts.join(';')
 
-    result, = @server.get(@prefix + '/das/' + dsn + '/sequence?' + query)
+    result, = Bio::Command.post_form("#{@server}/das/#{dsn}/sequence", opts)
     doc = REXML::Document.new(result.body)
     doc.elements.each('/descendant::SEQUENCE') do |e|
       sequence = SEQUENCE.new
@@ -188,9 +180,8 @@ class DAS
     segments.each do |s|
       opts << "segment=#{s.entry_id}:#{s.start},#{s.stop}"
     end
-    query = opts.join(';')
 
-    result, = @server.get(@prefix + '/das/' + dsn + '/types?' + query)
+    result, = Bio::Command.post_form("#{@server}/das/#{dsn}/types", opts)
     doc = REXML::Document.new(result.body)
     doc.elements.each('/descendant::GFF') do |e|
       types.version = e.attributes['version']
@@ -240,9 +231,8 @@ class DAS
     group_ids.each do |gid|
       opts << "group_id=#{gid}"
     end
-    query = opts.join(';')
 
-    result, = @server.get(@prefix + '/das/' + dsn + '/features?' + query)
+    result, = Bio::Command.post_form("#{@server}/das/#{dsn}/features", opts)
     doc = REXML::Document.new(result.body)
     doc.elements.each('/descendant::GFF') do |e|
       gff.version = e.attributes['version']
@@ -459,7 +449,7 @@ if __FILE__ == $0
   puts ">>> dsn : entry_points"
   org_list.each do |org|
     print "#{org} : "
-    list = kegg_das.get_entry_point(org)
+    list = kegg_das.get_entry_points(org)
     list.segments.each do |seg|
       print " #{seg.entry_id}"
     end

data/lib/bio/io/dbget.rb

@@ -4,33 +4,15 @@
 # Copyright::	Copyright (C) 2000, 2001
 #		Mitsuteru C. Nakao <n@bioruby.org>,
 #		Toshiaki Katayama <k@bioruby.org>
-# License::	LGPL
+# License::	The Ruby License
 #
-# $Id: dbget.rb,v 1.11 2005/11/05 08:32:26 k Exp $
+# $Id: dbget.rb,v 1.13 2007/04/05 23:35:41 trevor Exp $
 #
 # == DBGET
 #
 # Accessing the GenomeNet/DBGET data retrieval system
 # http://www.genome.jp/dbget/ within the intranet.
 #
-#--
-#
-#  This library is free software; you can redistribute it and/or
-#  modify it under the terms of the GNU Lesser General Public
-#  License as published by the Free Software Foundation; either
-#  version 2 of the License, or (at your option) any later version.
-#
-#  This library is distributed in the hope that it will be useful,
-#  but WITHOUT ANY WARRANTY; without even the implied warranty of
-#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-#  Lesser General Public License for more details.
-#
-#  You should have received a copy of the GNU Lesser General Public
-#  License along with this library; if not, write to the Free Software
-#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
-#
-#++
-#
 
 require 'socket'